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Journal articles on the topic 'DNA-ligand interactions'

Author: Grafiati

Published: 4 June 2021

Last updated: 20 February 2023

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1

Piosik, Jacek, Kacper Wasielewski, Anna Woziwodzka, Wojciech Śledź, and Anna Gwizdek-Wiśniewska. "De-intercalation of ethidium bromide and propidium iodine from DNA in the presence of caffeine." Open Life Sciences 5, no. 1 (February 1, 2010): 59–66. http://dx.doi.org/10.2478/s11535-009-0077-2.

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AbstractCaffeine (CAF) is capable of interacting directly with several genotoxic aromatic ligands by stacking aggregation. Formation of such hetero-complexes may diminish pharmacological activity of these ligands, which is often related to its direct interaction with DNA. To check these interactions we performed three independent series of spectroscopic titrations for each ligand (ethidium bromide, EB, and propidium iodine, PI) according to the following setup: DNA with ligand, ligand with CAF and DNA-ligand mixture with CAF. We analyzed DNA-ligand and ligand-CAF mixtures numerically using well known models: McGhee-von Hippel model for ligand-DNA interactions and thermodynamic-statistical model of mixed association of caffeine with aromatic ligands developed by Zdunek et al. (2000). Based on these models we calculated association constants and concentrations of mixture components using a novel method developed here. Results are in good agreement with parameters calculated in separate experiments and demonstrate de-intercalation of EB and PI molecules from DNA caused by CAF.

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2

Hopfinger, A. J., Mario G. Cardozo, and Y. Kawakami. "Molecular modelling of ligand–DNA intercalation interactions." J. Chem. Soc., Faraday Trans. 91, no. 16 (1995): 2515–24. http://dx.doi.org/10.1039/ft9959102515.

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3

Piehler, Jacob, Andreas Brecht, Günter Gauglitz, Marion Zerlin, Corinna Maul, Ralf Thiericke, and Susanne Grabley. "Label-Free Monitoring of DNA–Ligand Interactions." Analytical Biochemistry 249, no. 1 (June 1997): 94–102. http://dx.doi.org/10.1006/abio.1997.2160.

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4

van Royen, Martin E., Sónia M. Cunha, Maartje C. Brink, Karin A. Mattern, Alex L. Nigg, Hendrikus J. Dubbink, Pernette J. Verschure, Jan Trapman, and Adriaan B. Houtsmuller. "Compartmentalization of androgen receptor protein–protein interactions in living cells." Journal of Cell Biology 177, no. 1 (April 9, 2007): 63–72. http://dx.doi.org/10.1083/jcb.200609178.

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Steroid receptors regulate gene expression in a ligand-dependent manner by binding specific DNA sequences. Ligand binding also changes the conformation of the ligand binding domain (LBD), allowing interaction with coregulators via LxxLL motifs. Androgen receptors (ARs) preferentially interact with coregulators containing LxxLL-related FxxLF motifs. The AR is regulated at an extra level by interaction of an FQNLF motif in the N-terminal domain with the C-terminal LBD (N/C interaction). Although it is generally recognized that AR coregulator and N/C interactions are essential for transcription regulation, their spatiotemporal organization is largely unknown. We performed simultaneous fluorescence resonance energy transfer and fluorescence redistribution after photobleaching measurements in living cells expressing ARs double tagged with yellow and cyan fluorescent proteins. We provide evidence that AR N/C interactions occur predominantly when ARs are mobile, possibly to prevent unfavorable or untimely cofactor interactions. N/C interactions are largely lost when AR transiently binds to DNA, predominantly in foci partly overlapping transcription sites. AR coregulator interactions occur preferentially when ARs are bound to DNA.

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5

Adasme, Melissa F., Katja L. Linnemann, Sarah Naomi Bolz, Florian Kaiser, Sebastian Salentin, V. Joachim Haupt, and Michael Schroeder. "PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA." Nucleic Acids Research 49, W1 (May 5, 2021): W530—W534. http://dx.doi.org/10.1093/nar/gkab294.

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Abstract With the growth of protein structure data, the analysis of molecular interactions between ligands and their target molecules is gaining importance. PLIP, the protein–ligand interaction profiler, detects and visualises these interactions and provides data in formats suitable for further processing. PLIP has proven very successful in applications ranging from the characterisation of docking experiments to the assessment of novel ligand–protein complexes. Besides ligand–protein interactions, interactions with DNA and RNA play a vital role in many applications, such as drugs targeting DNA or RNA-binding proteins. To date, over 7% of all 3D structures in the Protein Data Bank include DNA or RNA. Therefore, we extended PLIP to encompass these important molecules. We demonstrate the power of this extension with examples of a cancer drug binding to a DNA target, and an RNA–protein complex central to a neurological disease. PLIP is available online at https://plip-tool.biotec.tu-dresden.de and as open source code. So far, the engine has served over a million queries and the source code has been downloaded several thousand times.

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6

Murade, Chandrashekhar U., and George T. Shubeita. "A fluorescent reporter on electrostatic DNA-ligand interactions." Biomedical Optics Express 13, no. 1 (December 7, 2021): 159. http://dx.doi.org/10.1364/boe.439791.

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7

Cremers, Glenn A. O., Bas J. H. M. Rosier, Ab Meijs, Nicholas B. Tito, Sander M. J. van Duijnhoven, Hans van Eenennaam, Lorenzo Albertazzi, and Tom F. A. de Greef. "Determinants of Ligand-Functionalized DNA Nanostructure–Cell Interactions." Journal of the American Chemical Society 143, no. 27 (June 28, 2021): 10131–42. http://dx.doi.org/10.1021/jacs.1c02298.

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8

Peterman, Erwin J. G., and Peter Gross. "Biophysics of DNA–ligand interactions resolved by force." Physics of Life Reviews 7, no. 3 (September 2010): 344–45. http://dx.doi.org/10.1016/j.plrev.2010.06.005.

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9

Murat, Pierre, Yashveer Singh, and Eric Defrancq. "Methods for investigating G-quadruplex DNA/ligand interactions." Chemical Society Reviews 40, no. 11 (2011): 5293. http://dx.doi.org/10.1039/c1cs15117g.

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10

Shi, Xuesong, and Robert B. Macgregor. "Volume and hydration changes of DNA–ligand interactions." Biophysical Chemistry 125, no. 2-3 (February 2007): 471–82. http://dx.doi.org/10.1016/j.bpc.2006.10.011.

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11

Pullman, Bernard. "Molecular mechanisms of specificity in DNA-ligand interactions." Journal of Molecular Graphics 7, no. 3 (September 1989): 181. http://dx.doi.org/10.1016/0263-7855(89)80045-1.

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12

Scheepers, M. R. W., L. J. van IJzendoorn, and M. W. J. Prins. "Multivalent weak interactions enhance selectivity of interparticle binding." Proceedings of the National Academy of Sciences 117, no. 37 (August 28, 2020): 22690–97. http://dx.doi.org/10.1073/pnas.2003968117.

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Targeted drug delivery critically depends on the binding selectivity of cargo-transporting colloidal particles. Extensive theoretical work has shown that two factors are necessary to achieve high selectivity for a threshold receptor density: multivalency and weak interactions. Here, we study a model system of DNA-coated particles with multivalent and weak interactions that mimics ligand–receptor interactions between particles and cells. Using an optomagnetic cluster experiment, particle aggregation rates are measured as a function of ligand and receptor densities. The measured aggregation rates show that the binding becomes more selective for shorter DNA ligand–receptor pairs, proving that multivalent weak interactions lead to enhanced selectivity in interparticle binding. Simulations confirm the experimental findings and show the role of ligand–receptor dissociation in the selectivity of the weak multivalent binding.

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13

Rahman, Khondaker M., and David E. Thurston. "Effect of microwave irradiation on covalent ligand–DNA interactions." Chemical Communications, no. 20 (2009): 2875. http://dx.doi.org/10.1039/b902357g.

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14

Nelson, Stephanie M., Lynnette R. Ferguson, and William A. Denny. "Non-covalent ligand/DNA interactions: Minor groove binding agents." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 623, no. 1-2 (October 2007): 24–40. http://dx.doi.org/10.1016/j.mrfmmm.2007.03.012.

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15

Nguyen, Binh, and W. David Wilson. "The Effects of Hairpin Loops on Ligand−DNA Interactions." Journal of Physical Chemistry B 113, no. 43 (October 29, 2009): 14329–35. http://dx.doi.org/10.1021/jp904830m.

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16

Howerton, Shelley B., Akankasha Nagpal, and Loren Dean Williams. "Surprising roles of electrostatic interactions in DNA-ligand complexes." Biopolymers 69, no. 1 (April 21, 2003): 87–99. http://dx.doi.org/10.1002/bip.10319.

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17

Savory, Joanne G. A., Gratien G. Préfontaine, Claudia Lamprecht, Mingmin Liao, Rhian F. Walther, Yvonne A. Lefebvre, and Robert J. G. Haché. "Glucocorticoid Receptor Homodimers and Glucocorticoid-Mineralocorticoid Receptor Heterodimers Form in the Cytoplasm through Alternative Dimerization Interfaces." Molecular and Cellular Biology 21, no. 3 (February 1, 2001): 781–93. http://dx.doi.org/10.1128/mcb.21.3.781-793.2001.

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ABSTRACT Steroid hormone receptors act to regulate specific gene transcription primarily as steroid-specific dimers bound to palindromic DNA response elements. DNA-dependent dimerization contacts mediated between the receptor DNA binding domains stabilize DNA binding. Additionally, some steroid receptors dimerize prior to their arrival on DNA through interactions mediated through the receptor ligand binding domain. In this report, we describe the steroid-induced homomeric interaction of the rat glucocorticoid receptor (GR) in solution in vivo. Our results demonstrate that GR interacts in solution at least as a dimer, and we have delimited this interaction to a novel interface within the hinge region of GR that appears to be both necessary and sufficient for direct binding. Strikingly, we also demonstrate an interaction between GR and the mineralocorticoid receptor in solution in vivo that is dependent on the ligand binding domain of GR alone and is separable from homodimerization of the glucocorticoid receptor. These results indicate that functional interactions between the glucocorticoid and mineralocorticoid receptors in activating specific gene transcription are probably more complex than has been previously appreciated.

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18

Mikheikin, A. L., A. L. Zhuze, and A. S. Zasedatelev. "Molecular Modelling of Ligand—DNA Minor Groove Binding: Role of Ligand—Water Interactions." Journal of Biomolecular Structure and Dynamics 19, no. 1 (August 2001): 175–78. http://dx.doi.org/10.1080/07391102.2001.10506729.

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19

Rocha, M. S. "Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments." Integrative Biology 7, no. 9 (2015): 967–86. http://dx.doi.org/10.1039/c5ib00127g.

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20

Berdnikova, Daria V., Tseimur M. Aliyeu, Thomas Paululat, Yuri V. Fedorov, Olga A. Fedorova, and Heiko Ihmels. "DNA–ligand interactions gained and lost: light-induced ligand redistribution in a supramolecular cascade." Chemical Communications 51, no. 23 (2015): 4906–9. http://dx.doi.org/10.1039/c5cc01025j.

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21

Fong, Pedro, and Hong-Kong Wong. "Evaluation of Scoring Function Performance on DNA-ligand Complexes." Open Medicinal Chemistry Journal 13, no. 1 (July 31, 2019): 40–49. http://dx.doi.org/10.2174/1874104501913010040.

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Background: DNA has been a pharmacological target for different types of treatment, such as antibiotics and chemotherapy agents, and is still a potential target in many drug discovery processes. However, most docking and scoring approaches were parameterised for protein-ligand interactions; their suitability for modelling DNA-ligand interactions is uncertain. Objective: This study investigated the performance of four scoring functions on DNA-ligand complexes. Material & Methods: Here, we explored the ability of four docking protocols and scoring functions to discriminate the native pose of 33 DNA-ligand complexes over a compiled set of 200 decoys for each DNA-ligand complexes. The four approaches were the AutoDock, ASP@GOLD, ChemScore@GOLD and GoldScore@GOLD. Results: Our results indicate that AutoDock performed the best when predicting binding mode and that ChemScore@GOLD achieved the best discriminative power. Rescoring of AutoDock-generated decoys with ChemScore@GOLD further enhanced their individual discriminative powers. All four approaches have no discriminative power in some DNA-ligand complexes, including both minor groove binders and intercalators. Conclusion: This study suggests that the evaluation for each DNA-ligand complex should be performed in order to obtain meaningful results for any drug discovery processes. Rescoring with different scoring functions can improve discriminative power.

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22

Shahabadi, Nahid, Soheila Kashanian, Maryam Mahdavi, and Noorkaram Sourinejad. "DNA Interaction and DNA Cleavage Studies of a New Platinum(II) Complex Containing Aliphatic and Aromatic Dinitrogen Ligands." Bioinorganic Chemistry and Applications 2011 (2011): 1–10. http://dx.doi.org/10.1155/2011/525794.

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A new Pt(II) complex, [Pt(DIP)(LL)](NO3)2(in which DIP is 4,7-diphenyl-1,10-phenanthroline and LL is the aliphatic dinitrogen ligand,N,N-dimethyl-trimethylenediamine), was synthesized and characterized using different physico-chemical methods. The interaction of this complex with calf thymus DNA (CT-DNA) was investigated by absorption, emission, circular dichroism (CD), and viscosity measurements. The complex binds to CT-DNA in an intercalative mode. The calculated binding constant,Kb, was M−1. The enthalpy and entropy changes of the reaction between the complex and CT-DNA showed that the van der Waals interactions and hydrogen bonds are the main forces in the interaction with CT-DNA. In addition, CD study showed that phenanthroline ligand insert between the base pair stack of double helical structure of DNA. It is remarkable that this complex has the ability to cleave the supercoiled plasmid.

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23

Brodbelt, Jennifer S. "Evaluation of DNA/Ligand Interactions by Electrospray Ionization Mass Spectrometry." Annual Review of Analytical Chemistry 3, no. 1 (June 2010): 67–87. http://dx.doi.org/10.1146/annurev.anchem.111808.073627.

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24

Rentzeperis, Dionisios, Luis A. Marky, and Donald W. Kupke. "Entropy-volume correlation with hydration changes in DNA-ligand interactions." Journal of Physical Chemistry 96, no. 24 (November 1992): 9612–13. http://dx.doi.org/10.1021/j100203a011.

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25

Cabeza de Vaca, Israel, Maria Fátima Lucas, and Victor Guallar. "New Monte Carlo Based Technique To Study DNA–Ligand Interactions." Journal of Chemical Theory and Computation 11, no. 12 (November 11, 2015): 5598–605. http://dx.doi.org/10.1021/acs.jctc.5b00838.

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26

Murat, Pierre, Yashveer Singh, and Eric Defrancq. "ChemInform Abstract: Methods for Investigating G-Quadruplex DNA/Ligand Interactions." ChemInform 43, no. 3 (December 22, 2011): no. http://dx.doi.org/10.1002/chin.201203280.

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27

Chirivino, Emanuele, Cesare Giordano, Sara Faini, Luciano Cellai, and Marco Fragai. "Tuning Sensitivity in Paramagnetic NMR Detection of Ligand–DNA Interactions." ChemMedChem 2, no. 8 (August 13, 2007): 1153–56. http://dx.doi.org/10.1002/cmdc.200600311.

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28

Khan, Sabab Hasan, and C. Denise Okafor. "Interactions governing transcriptional activity of nuclear receptors." Biochemical Society Transactions 50, no. 6 (December 16, 2022): 1941–52. http://dx.doi.org/10.1042/bst20220338.

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The key players in transcriptional regulation are transcription factors (TFs), proteins that bind specific DNA sequences. Several mechanisms exist to turn TFs ‘on’ and ‘off’, including ligand binding which induces conformational changes within TFs, subsequently influencing multiple inter- and intramolecular interactions to drive transcriptional responses. Nuclear receptors are a specific family of ligand-regulated TFs whose activity relies on interactions with DNA, coregulator proteins and other receptors. These multidomain proteins also undergo interdomain interactions on multiple levels, further modulating transcriptional outputs. Cooperation between these distinct interactions is critical for appropriate transcription and remains an intense area of investigation. In this review, we report and summarize recent findings that continue to advance our mechanistic understanding of how interactions between nuclear receptors and diverse partners influence transcription.

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29

Yusof, Enis Nadia Md, Mohammad Azam, Siti Syaida Sirat, Thahira B. S. A. Ravoof, Alister J. Page, Abhi Veerakumarasivam, Thiruventhan Karunakaran, and Mohd Rizal Razali. "Dithiocarbazate Ligand-Based Cu(II), Ni(II), and Zn(II) Complexes: Synthesis, Structural Investigations, Cytotoxicity, DNA Binding, and Molecular Docking Studies." Bioinorganic Chemistry and Applications 2022 (July 31, 2022): 1–13. http://dx.doi.org/10.1155/2022/2004052.

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S-4-methylbenzyl-β-N-(2-methoxybenzylmethylene)dithiocarbazate ligand, 1, prepared from S-(4-methylbenzyl)dithiocarbazate, was used to produce a novel series of transition metal complexes of the type, [M (L)2] [M = Cu(II) (2), Ni(II) (3), and Zn(II) (4), L = 1]. The ligand and its complexes were investigated by elemental analysis, FTIR, 1H and 13C-NMR, MS spectrometry, and molar conductivity. In addition, single X-ray crystallography was also performed for ligand, 1, and complex 3. The Hirshfeld surface analyses were also performed to know about various bonding interactions in the ligand, 1, and complex 3. The investigated compounds were also tested to evaluate their cytotoxic behaviour. However, complex 2 showed promising results against MCF-7 and MDA-MB-213 cancer cell lines. Furthermore, the interaction of CT-DNA with ligand, 1, and complex 2 was also studied using the electronic absorption method, revealing that the compounds have potential DNA-binding ability via hydrogen bonding and hydrophobic and van der Waals interactions. A molecular docking study of complex 2 was also carried out, which revealed that free binding free energy value was −7.39 kcal mol−1.

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30

Linne, Christine, Daniele Visco, Stefano Angioletti-Uberti, Liedewij Laan, and Daniela J. Kraft. "Direct visualization of superselective colloid-surface binding mediated by multivalent interactions." Proceedings of the National Academy of Sciences 118, no. 36 (August 31, 2021): e2106036118. http://dx.doi.org/10.1073/pnas.2106036118.

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Reliably distinguishing between cells based on minute differences in receptor density is crucial for cell–cell or virus–cell recognition, the initiation of signal transduction, and selective targeting in directed drug delivery. Such sharp differentiation between different surfaces based on their receptor density can only be achieved by multivalent interactions. Several theoretical and experimental works have contributed to our understanding of this “superselectivity.” However, a versatile, controlled experimental model system that allows quantitative measurements on the ligand–receptor level is still missing. Here, we present a multivalent model system based on colloidal particles equipped with surface-mobile DNA linkers that can superselectively target a surface functionalized with the complementary mobile DNA-linkers. Using a combined approach of light microscopy and Foerster resonance energy transfer (FRET), we can directly observe the binding and recruitment of the ligand–receptor pairs in the contact area. We find a nonlinear transition in colloid-surface binding probability with increasing ligand or receptor concentration. In addition, we observe an increased sensitivity with weaker ligand–receptor interactions, and we confirm that the timescale of binding reversibility of individual linkers has a strong influence on superselectivity. These unprecedented insights on the ligand–receptor level provide dynamic information into the multivalent interaction between two fluidic membranes mediated by both mobile receptors and ligands and will enable future work on the role of spatial–temporal ligand–receptor dynamics on colloid-surface binding.

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31

Chernikova, Ekaterina Y., Anna Y. Ruleva, Vladimir B. Tsvetkov, Yuri V. Fedorov, Valentin V. Novikov, Tseimur M. Aliyeu, Alexander A. Pavlov, Nikolay E. Shepel, and Olga A. Fedorova. "Cucurbit[7]uril-driven modulation of ligand–DNA interactions by ternary assembly." Organic & Biomolecular Chemistry 18, no. 4 (2020): 755–66. http://dx.doi.org/10.1039/c9ob02543j.

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32

Kobren, Shilpa Nadimpalli, and Mona Singh. "Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions." Nucleic Acids Research 47, no. 2 (December 7, 2018): 582–93. http://dx.doi.org/10.1093/nar/gky1224.

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Abstract Domains are fundamental subunits of proteins, and while they play major roles in facilitating protein–DNA, protein–RNA and other protein–ligand interactions, a systematic assessment of their various interaction modes is still lacking. A comprehensive resource identifying positions within domains that tend to interact with nucleic acids, small molecules and other ligands would expand our knowledge of domain functionality as well as aid in detecting ligand-binding sites within structurally uncharacterized proteins. Here, we introduce an approach to identify per-domain-position interaction ‘frequencies’ by aggregating protein co-complex structures by domain and ascertaining how often residues mapping to each domain position interact with ligands. We perform this domain-based analysis on ∼91000 co-complex structures, and infer positions involved in binding DNA, RNA, peptides, ions or small molecules across 4128 domains, which we refer to collectively as the InteracDome. Cross-validation testing reveals that ligand-binding positions for 2152 domains are highly consistent and can be used to identify residues facilitating interactions in ∼63–69% of human genes. Our resource of domain-inferred ligand-binding sites should be a great aid in understanding disease etiology: whereas these sites are enriched in Mendelian-associated and cancer somatic mutations, they are depleted in polymorphisms observed across healthy populations. The InteracDome is available at http://interacdome.princeton.edu.

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33

Cheskis, B., and L. P. Freedman. "Ligand modulates the conversion of DNA-bound vitamin D3 receptor (VDR) homodimers into VDR-retinoid X receptor heterodimers." Molecular and Cellular Biology 14, no. 5 (May 1994): 3329–38. http://dx.doi.org/10.1128/mcb.14.5.3329-3338.1994.

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Protein dimerization facilitates cooperative, high-affinity interactions with DNA. Nuclear hormone receptors, for example, bind either as homodimers or as heterodimers with retinoid X receptors (RXR) to half-site repeats that are stabilized by protein-protein interactions mediated by residues within both the DNA- and ligand-binding domains. In vivo, ligand binding among the subfamily of steroid receptors unmasks the nuclear localization and DNA-binding domains from a complex with auxiliary factors such as the heat shock proteins. However, the role of ligand is less clear among nuclear receptors, since they are constitutively localized to the nucleus and are presumably associated with DNA in the absence of ligand. In this study, we have begun to explore the role of the ligand in vitamin D3 receptor (VDR) function by examining its effect on receptor homodimer and heterodimer formation. Our results demonstrate that VDR is a monomer in solution; VDR binding to a specific DNA element leads to the formation of a homodimeric complex through a monomeric intermediate. We find that 1,25-dihydroxyvitamin D3, the ligand for VDR, decreases the amount of the DNA-bound VDR homodimer complex. It does so by significantly decreasing the rate of conversion of DNA-bound monomer to homodimer and at the same time enhancing the dissociation of the dimeric complex. This effectively stabilizes the bound monomeric species, which in turn serves to favor the formation of a VDR-RXR heterodimer. The ligand for RXR, 9-cis retinoic acid, has the opposite effect of destabilizing the heterodimeric-DNA complex. These results may explain how a nuclear receptor can bind DNA constitutively but still act to regulate transcription in a fully hormone-dependent manner.

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34

Cheskis, B., and L. P. Freedman. "Ligand modulates the conversion of DNA-bound vitamin D3 receptor (VDR) homodimers into VDR-retinoid X receptor heterodimers." Molecular and Cellular Biology 14, no. 5 (May 1994): 3329–38. http://dx.doi.org/10.1128/mcb.14.5.3329.

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Protein dimerization facilitates cooperative, high-affinity interactions with DNA. Nuclear hormone receptors, for example, bind either as homodimers or as heterodimers with retinoid X receptors (RXR) to half-site repeats that are stabilized by protein-protein interactions mediated by residues within both the DNA- and ligand-binding domains. In vivo, ligand binding among the subfamily of steroid receptors unmasks the nuclear localization and DNA-binding domains from a complex with auxiliary factors such as the heat shock proteins. However, the role of ligand is less clear among nuclear receptors, since they are constitutively localized to the nucleus and are presumably associated with DNA in the absence of ligand. In this study, we have begun to explore the role of the ligand in vitamin D3 receptor (VDR) function by examining its effect on receptor homodimer and heterodimer formation. Our results demonstrate that VDR is a monomer in solution; VDR binding to a specific DNA element leads to the formation of a homodimeric complex through a monomeric intermediate. We find that 1,25-dihydroxyvitamin D3, the ligand for VDR, decreases the amount of the DNA-bound VDR homodimer complex. It does so by significantly decreasing the rate of conversion of DNA-bound monomer to homodimer and at the same time enhancing the dissociation of the dimeric complex. This effectively stabilizes the bound monomeric species, which in turn serves to favor the formation of a VDR-RXR heterodimer. The ligand for RXR, 9-cis retinoic acid, has the opposite effect of destabilizing the heterodimeric-DNA complex. These results may explain how a nuclear receptor can bind DNA constitutively but still act to regulate transcription in a fully hormone-dependent manner.

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35

Pohle, W., and H. Fritzsche. "Infrared spectroscopy as a tool for investigations of DNA structure and DNA - ligand interactions." Journal of Molecular Structure 219 (March 1990): 341–46. http://dx.doi.org/10.1016/0022-2860(90)80079-y.

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36

Issa, Naiem T., Stephen W. Byers, and Sivanesan Dakshanamurthy. "ES-Screen: A Novel Electrostatics-Driven Method for Drug Discovery Virtual Screening." International Journal of Molecular Sciences 23, no. 23 (November 27, 2022): 14830. http://dx.doi.org/10.3390/ijms232314830.

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Electrostatic interactions drive biomolecular interactions and associations. Computational modeling of electrostatics in biomolecular systems, such as protein-ligand, protein–protein, and protein-DNA, has provided atomistic insights into the binding process. In drug discovery, finding biologically plausible ligand-protein target interactions is challenging as current virtual screening and adjuvant techniques such as docking methods do not provide optimal treatment of electrostatic interactions. This study describes a novel electrostatics-driven virtual screening method called ‘ES-Screen’ that performs well across diverse protein target systems. ES-Screen provides a unique treatment of electrostatic interaction energies independent of total electrostatic free energy, typically employed by current software. Importantly, ES-Screen uses initial ligand pose input obtained from a receptor-based pharmacophore, thus independent of molecular docking. ES-Screen integrates individual polar and nonpolar replacement energies, which are the energy costs of replacing the cognate ligand for a target with a query ligand from the screening. This uniquely optimizes thermodynamic stability in electrostatic and nonpolar interactions relative to an experimentally determined stable binding state. ES-Screen also integrates chemometrics through shape and other physicochemical properties to prioritize query ligands with the greatest physicochemical similarities to the cognate ligand. The applicability of ES-Screen is demonstrated with in vitro experiments by identifying novel targets for many drugs. The present version includes a combination of many other descriptor components that, in a future version, will be purely based on electrostatics. Therefore, ES-Screen is a first-in-class unique electrostatics-driven virtual screening method with a unique implementation of replacement electrostatic interaction energies with broad applicability in drug discovery.

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37

Rodrigues, Tatiane P., Jorddy N. Cruz, Tiago S. Arouche, Tais S. S. Pereira, Wanessa A. Costa, Sebastião G. Silva, Raul N. C. Junior, Mozaniel S. Oliveira, and Antonio M. J. C. Neto. "Molecular Modeling Approach to Investigate the Intercalation of Phthalates and Their Metabolites in DNA Macromolecules." Journal of Computational and Theoretical Nanoscience 16, no. 2 (February 1, 2019): 373–80. http://dx.doi.org/10.1166/jctn.2019.8110.

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Recent studies have reported that phthalates are capable of causing mutations and other changes in the genetic material. This study aimed to investigate the molecular interactions between phthalate di(2-ethylhexyl) phthalate (DEHP) and its metabolites monobutyl phthalate (MBP) and monoethyl phthalate (MEP), interacting with DNA. The research was conducted using molecular modeling techniques such as molecular docking and molecular dynamics simulations. Molecular docking revealed that the DEHP, MBP, and MEP are able to establish hydrogen interactions with various nucleotide bases. Molecular dynamics simulations revealed that these molecules interacted with the DNA, and the binding free energy results demonstrated that the DNA-ligand interaction has favorable free energy. The values for free binding energy were as follows: DNA–DEHP, –21.66 kcal/mol; DNA–MBP, –17.29 kcal/mol; and DNA–MEP, –20.13 kcal/mol. For these three systems, the contributions of van der Waals, electrostatic, and nonpolar solvation energy were favorable for the interaction. The van der Waals interactions contributed the major energy to the intercalation of the binders.

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Mie, Masayasu, Rie Sugita, Tamaki Endoh, and Eiry Kobatake. "Evaluation of small ligand–protein interactions by using T7 RNA polymerase with DNA-modified ligand." Analytical Biochemistry 405, no. 1 (October 2010): 109–13. http://dx.doi.org/10.1016/j.ab.2010.06.011.

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Przibilla, S., W. W. Hitchcock, M. Szécsi, M. Grebe, J. Beatty, V. C. Henrich, and M. Spindler-Barth. "Functional studies on the ligand-binding domain of Ultraspiracle from Drosophila melanogaster." Biological Chemistry 385, no. 1 (January 5, 2004): 21–30. http://dx.doi.org/10.1515/bc.2004.004.

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AbstractThe functional insect ecdysteroid receptor is comprised of the ecdysone receptor (EcR) and Ultraspiracle (USP). The ligand-binding domain (LBD) of USP was fused to the GAL4 DNA-binding domain (GAL4-DBD) and characterized by analyzing the effect of site-directed mutations in the LBD. Normal and mutant proteins were tested for ligand and DNA binding, dimerization, and their ability to induce gene expression. The presence of helix 12 proved to be essential for DNA binding and was necessary to confer efficient ecdysteroid binding to the heterodimer with the EcR (LBD), but did not influence dimerization. The antagonistic position of helix 12 is indispensible for interaction between the fusion protein and DNA, whereas hormone binding to the EcR (LBD) was only partially reduced if fixation of helix 12 was disturbed. The mutation of amino acids, which presumably bind to a fatty acid evoked a profound negative influence on transactivation ability, although enhanced transactivation potency and ligand binding to the ecdysteroid receptor was impaired to varying degrees by mutation of these residues. Mutations of one fatty acidbinding residue within the ligand-binding pocket, I323, however, evoked enhanced transactivation. The results confirmed that the LBD of Ultraspiracle modifies ecdysteroid receptor function through intermolecular interactions and demonstrated that the ligand-binding pocket of USP modifies the DNA-binding and transactivation abilities of the fusion protein.

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Joachimiak, Andrzej, Grazyna Joachimiak, Lance Bigelow, Garrett Cobb, and Youngchang Kim. "HcaR Ligand and DNA Interactions in the Regulation of Catabolic Gene Expression." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C203. http://dx.doi.org/10.1107/s2053273314097964.

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Precise tuning of gene expression by transcriptional regulators determines the response to internal and external chemical signals and adjusts the metabolic machinery for many cellular processes. As a part of ongoing efforts by the Midwest Center for Structural Genomics, a number of transcription factors were selected to study protein-ligand and protein-DNA interactions. HcaR, a new member of the MarR/SlyA family of transcription regulators from soil bacteria Acinetobacter sp. ADP1, is an evolutionarily atypical regulator and represses hydroxycinnamate (hca) catabolic genes. Hydroxycinnamates containing an aromatic ring play diverse, critical roles in plant architecture and defense. HcaR regulates the expression of the hca catabolic operon, allowing this and related bacterial strains to utilize hydroxycinnamates: ferulate, p-coumarate, and caffeate as sole sources of carbon and energy. HcaR appears to be capable of responding to multiple aromatic ligands. These aromatic compounds bind to HcaR and reduce its affinity to the specific DNA sites. As a result, the transcription of genes encoding several catabolic enzymes is up-regulated. The HcaR structures of the apo-form and in a complex with several ligands: ferulic acid, 3,4 dihydroxybenzoic acid, vanillin and p-coumaric acid have been determined to understand how HcaR accommodates various aromatic compounds using the same binding pocket. We also have identified a potential DNA site for HcaR in the regulatory region upstream of the genes of the hca catabolic operon in Acinetobacter sp. ADP1 and have confirmed DNA binding by EMSA. The co-crystal structure of HcaR and palindromic 24-mer DNA has been determined for this DNA site. The crystal structures of HcaR, the apo-form, ligand-bound forms, and the specific DNA-bound form provide critical structural basis of protein-ligand (substrates or product) and protein-DNA interactions to understand the regulation of the expression of hydroxycinnamate (hca) catabolic genes. Our studies allow for better understanding of DNA-binding and regulation by this important group of transcription factors belonging to the MarR/SlyA families. This work was supported by National Institutes of Health grant GM094585 and by the U. S. Department of Energy, Office of Biological and Environmental Research, under contract DE-AC02-06CH11357.

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Li, Min, Hongming Ding, Meihua Lin, Fangfei Yin, Lu Song, Xiuhai Mao, Fan Li, et al. "DNA Framework-Programmed Cell Capture via Topology-Engineered Receptor–Ligand Interactions." Journal of the American Chemical Society 141, no. 47 (November 6, 2019): 18910–15. http://dx.doi.org/10.1021/jacs.9b11015.

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Hamdan, I. I., G. G. Skellern, and R. D. Waigh. "Use of capillary electrophoresis in the study of ligand-DNA interactions." Nucleic Acids Research 26, no. 12 (June 1, 1998): 3053–58. http://dx.doi.org/10.1093/nar/26.12.3053.

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Misra, V. K., and B. Honig. "On the magnitude of the electrostatic contribution to ligand-DNA interactions." Proceedings of the National Academy of Sciences 92, no. 10 (May 9, 1995): 4691–95. http://dx.doi.org/10.1073/pnas.92.10.4691.

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Kupferschmitt, G., J. Schmidt, Th Schmidt, B. Fera, F. Buck, and H. Riiterjans. "15N labeling of oligodeoxynucleotides for NMR studies of DNA-ligand interactions." Nucleic Acids Research 15, no. 15 (1987): 6225–41. http://dx.doi.org/10.1093/nar/15.15.6225.

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Krafcikova, Michaela, Simon Dzatko, Coralie Caron, Anton Granzhan, Radovan Fiala, Tomas Loja, Marie-Paule Teulade-Fichou, et al. "Monitoring DNA–Ligand Interactions in Living Human Cells Using NMR Spectroscopy." Journal of the American Chemical Society 141, no. 34 (August 9, 2019): 13281–85. http://dx.doi.org/10.1021/jacs.9b03031.

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Mahapatra, Tufan Singha, Susmitnarayan Chaudhury, Swagata Dasgupta, Valerio Bertolasi, and Debashis Ray. "Dinuclear nickel complexes of divergent Ni⋯Ni separation showing ancillary ligand addition and bio-macromolecular interaction." New Journal of Chemistry 40, no. 3 (2016): 2268–79. http://dx.doi.org/10.1039/c5nj02410b.

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Reactions of ligand HL with nickel(ii) salts produce a family of five [Ni₂] complexes of varying co-ligand environments and intermetallic separations and show prominent interactions with HSA and CT-DNA.

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Banasiak, Anna, Nicolò Zuin Fantoni, Andrew Kellett, and John Colleran. "Mapping the DNA Damaging Effects of Polypyridyl Copper Complexes with DNA Electrochemical Biosensors." Molecules 27, no. 3 (January 19, 2022): 645. http://dx.doi.org/10.3390/molecules27030645.

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Several classes of copper complexes are known to induce oxidative DNA damage that mediates cell death. These compounds are potentially useful anticancer agents and detailed investigation can reveal the mode of DNA interaction, binding strength, and type of oxidative lesion formed. We recently reported the development of a DNA electrochemical biosensor employed to quantify the DNA cleavage activity of the well-studied [Cu(phen)2]2+ chemical nuclease. However, to validate the broader compatibility of this sensor for use with more diverse—and biologically compatible—copper complexes, and to probe its use from a drug discovery perspective, analysis involving new compound libraries is required. Here, we report on the DNA binding and quantitative cleavage activity of the [Cu(TPMA)(N,N)]2+ class (where TPMA = tris-2-pyridylmethylamine) using a DNA electrochemical biosensor. TPMA is a tripodal copper caging ligand, while N,N represents a bidentate planar phenanthrene ligand capable of enhancing DNA interactions through intercalation. All complexes exhibited electroactivity and interact with DNA through partial (or semi-) intercalation but predominantly through electrostatic attraction. Although TPMA provides excellent solution stability, the bulky ligand enforces a non-planar geometry on the complex, which sterically impedes full interaction. [Cu(TPMA)(phen)]2+ and [Cu(TPMA)(DPQ)]2+ cleaved 39% and 48% of the DNA strands from the biosensor surface, respectively, while complexes [Cu(TPMA)(bipy)]2+ and [Cu(TPMA)(PD)]2+ exhibit comparatively moderate nuclease efficacy (ca. 26%). Comparing the nuclease activities of [Cu(TPMA)(phen)] 2+ and [Cu(phen)2]2+ (ca. 23%) confirms the presence of TPMA significantly enhances chemical nuclease activity. Therefore, the use of this DNA electrochemical biosensor is compatible with copper(II) polypyridyl complexes and reveals TPMA complexes as a promising class of DNA damaging agent with tuneable activity due to coordinated ancillary phenanthrene ligands.

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Gautam, Pankaj, and Sudipta Kumar Sinha. "Anticipating response function in gene regulatory networks." Journal of The Royal Society Interface 18, no. 179 (June 2021): 20210206. http://dx.doi.org/10.1098/rsif.2021.0206.

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The origin of an ordered genetic response of a complex and noisy biological cell is intimately related to the detailed mechanism of protein–DNA interactions present in a wide variety of gene regulatory (GR) systems. However, the quantitative prediction of genetic response and the correlation between the mechanism and the response curve is poorly understood. Here, we report in silico binding studies of GR systems to show that the transcription factor (TF) binds to multiple DNA sites with high cooperativity spreads from specific binding sites into adjacent non-specific DNA and bends the DNA. Our analysis is not limited only to the isolated model system but also can be applied to a system containing multiple interacting genes. The controlling role of TF oligomerization, TF–ligand interactions, and DNA looping for gene expression has been also characterized. The predictions are validated against detailed grand canonical Monte Carlo simulations and published data for the lac operon system. Overall, our study reveals that the expression of target genes can be quantitatively controlled by modulating TF–ligand interactions and the bending energy of DNA.

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Chao, Hui, and Liang-Nian Ji. "DNA Interactions with Ruthenium(II) Polypyridine Complexes Containing Asymmetric Ligands." Bioinorganic Chemistry and Applications 3, no. 1-2 (2005): 15–28. http://dx.doi.org/10.1155/bca.2005.15.

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In an attempt to probe nucleic acid structures, numerous Ru(II) complexes with different ligands have been synthesized and investigated. In this contribution we focus on the DNA-binding properties of ruthenium(II) complexes containing asymmetric ligands that have attracted little attention in the past decades. The influences of the shape and size of the ligand on the binding modes, affinity, enantioselectivities and photocleavage of the complexes to DNA are described.

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Ihmels, H., M. Karbasiyoun, K. Löhl, and C. Stremmel. "Structural flexibility versus rigidity of the aromatic unit of DNA ligands: binding of aza- and azoniastilbene derivatives to duplex and quadruplex DNA." Organic & Biomolecular Chemistry 17, no. 26 (2019): 6404–13. http://dx.doi.org/10.1039/c9ob00809h.

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The increased flexibility of a quadruplex-DNA ligand does not necessarily lead to stronger interactions with the quadruplex DNA as compared with rigid ligands that have essentially the same size and extent of π system.

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